Output Handling

This takes an anno file as input at any stage and properly annotates it for compatability with shiny and other scrattch functions. In particular, it ensures that columns have a label, an id, and a color, and that there are no factors. It won't overwrite columns that have already been properly process.

auto_annotate(anno, scale_num = "predicted", na_val_num = 0,
  colorset_num = c("darkblue", "white", "red"), sort_label_cat = TRUE,
  na_val_cat = "ZZ_Missing", colorset_cat = "varibow",
  color_order_cat = "sort")

`anno`	an existing annotation data frame
`scale_num`	should color scaling of numeric values be "predicted" (default and highly recommended; will return either "linear" or "log10" depending on scaling), "linear","log10","log2", or "zscore".
`na_val_num`	The value to use to replace NAs for numeric columns. default = 0.
`colorset_num`	A vector of colors to use for the color gradient. default = c("darkblue","white","red")
`sort_label_cat`	a logical value to determine if the data in category columns should be arranged alphanumerically before ids are assigned. default = T.
`na_val_cat`	The value to use to replace NAs in category and factor variables. default = "ZZ_Missing".
`colorset_cat`	The colorset to use for assigning category and factor colors. Options are "varibow" (default), "rainbow","viridis","inferno","magma", and "terrain"
`color_order_cat`	The order in which colors should be assigned for cat and factor variables. Options are "sort" and "random". "sort" (default) assigns colors in order; "random" will randomly assign colors.